Frequently Asked Questions (FAQs) about V-Track
Here are some of the most common problems that users are having when using V-Track. If you cannot find an answer to your problem here, email firstname.lastname@example.org
Q: How do I download V-Track?
A: Go to the website http://www.uq.edu.au/eco-lab/v-track and follow the instructions.
Q: V-Track won't run with the new versions of R (>= v 3.0.0), How can I get V-Track to run on my machine?
A: We have recently updated the V-Track (now V-Track version 1.02) which works under this new platform.
Q: When I export the CSV file of the detection data data from VUE 3 it will not load into V-Track.
A: this is because the file format for VUE3 is different from previous versions of VUE. Those nice guys at VEMCO have however, included an option in VUE3 to export CSV data in the older format. Open the <file> drop down window, then select <options>, open up the <export> tab and change export from the "Default" to "Version 1.0 format". The next upgrade of V-Track will allow for Vue 3 dection data format.
# Note. V-Track >v1.01 now has an option in both the R package and the GUI whereby the user can distinguish between the "Default" VUE export format and the "Version 1.0" format when running the ReadInputData function (Step 1: Add to archive).
Q: I opened my CSV fiel in EXCEL to edit and now it will not load into V-Track.
A: Once a CSV is opened in EXCEL it alters the date/time format to EXCELS own reference system. Although the data/time format looks the same it is comma rather than tab delimited. Instructions on how to fix this are in the V-Track user manual.
Q: When I run step 3: generate a distance matrix no file is returned.
A: This may occur for a number of reasons. 1/ Are the headings in the points file uppercase and exactly as they appear in the manual. 2/ Are you Geographic Coordinates in decimal degrees. 3/ Do you have a valuefor all the receiver detection radii (even if it is 0).
Q:How do I calculate the receiver distance matrix for receivers that are distributed along a river system or coastline?
A: Use the function GenerateCircuitousDistance in the receiver distance matrix calculator of (step 3 in the V-Track GUI).
Q:How do I calculate the receiver distance matrix for receivers that are distributed in a grid system?
A: Use the function GenerateDirectDistance in the receiver distance matrix calculator of (step 3 in the V-Track GUI). If your receiver detection radii overlap, then a single pulse will be detected at more than one receiver. This will result in very short residence events, or none at all. We are working on solving this problem soon.
Q: I wish to calculate a circuitious receiver distance matrix, but some of the receivers are placed long different branches of a river.
A: It was not possible for V-track to code for every type fo receiver array. So we have included an option for the user to edit the RDM file after it has been created. This will allow additional receivers to be added once the main array arrangement has been calculated. See section 3.3 of user manual.
Q: When I run Step 4. Extract Events with a recevier distance matrix (RDM) no file is returned.
A: This can occur if the RDM does not have the identical recevier IDs or station names that are found within the detection archive. We suggest run the extract events without the RDM included to ensure that this is the problem. If the events are extracted without the distance matrix, then check the RDM file is correct. If you exported your detection data from VUE in the 'Default' format, make sure that your POINTS file also contains the "VR2W-" characters, which precede the receiver ID. Other receivers can be added manually into the RDM.
Q: When I extract residence and movement events using V-Track very few events are identified, even through my animals are moving between the receviers.
A: When the receiver array has over-lapping detection areas it is possible for a single transmission to be detected upon more than one receiver. To extract a residence event V-track needs to observe a minimum of two detections at each receiver (when animal entered and departed the recevier detection area). When the recevier detection areas are overlapping the double detection of each transmission prevents V-track from recording thisd residence event. The solution would be to remove the data from one of the receivers using step 2 in V-track, then run the residence event function. For the same reason the movement events will not be calculated by V-Track because reseidence events are required by V-Track to calculate the animal's movement between receiver detection fields. We are working on a new module to solve this issue, stay tuned.
Q: How do I extract behavioural events from a subset of receivers in my array?
A: Use the ExtractData function (step 2 in the V-Track GUI), and specify the subset of receivers that you want to extract data for. Then use the Behavioural Event Qualifier to analyse your subset of data (step 4 in the V-Track GUI).
Q:The animation file in Google Earth runs too fast to see what is happening.
A: You can slow it down in the tools in Google Earth. You can reduce the time span of the events you are viewing to slow the animation further.
Q: My data is taking a long time to load, or V-Track crashes while trying to analyse my data.
A: Acoustic detection files typically consist of thousands or millions of detections and V-track examines these through a moving window on a line by line basis. To speed up the process 1/ extract a smaller subset of data in step 2 for analysis. 2/ A good idea is to create a smaller detection archive consisting of detections from only one animal (step 2) and use this as your test file in later analysis steps. This ensures that the procedures are running OK before you run a much larger file that may take many hours to run. The analysis time of V-track can reduced, and more than one V-Track analysis run if you use a computer with multiple processors. Future developments for V-Track are to increase performance and analysis speed.
Q: The study site is a branched river system comprising of two waterways with receivers deployed in both waterways.
A: The distance matrix algorithm within V-Track can only calculates circuitous distances correctly if the acoustic array exists in a single trunk of river. If the array is within multiple river branches each branch must be calculated independantly and then the two RDM amalgamated. You can manually add or substract receivers from the RDM.
Q: When I run the 'GenerateCircuitousDistance' function, I receive the error - 'Error in '[<-'('*tmp*', i + 1, j, value = ...) : subscript out of bounds.'
A: This error occurs because R is looking for additional waypoints (RECEIVERID = 0) which lie between your receivers. This functionality was added to support its application to rivers with meanders between receiver stations. If you add a single additional waypoints to your points file, this will solve this issue and you will be able to generate your circuitous distance matrix.
Q: When I try to install the VTrack package I get the error message: 'ERROR: dependencies 'foreach', 'doMC'... ' are not available for package 'VTrack'.
A: VTrack is dependant on these R packages in order to run. You therefore need to download them into your R package library before running VTrack.
Try typing the below code into R - it's a shortcut to download the packages off the Melbourne CRAN repository
## On Windows
install.packages(c('sp','rgdal','spatstat','RColorBrewer','googleVis','rgeos'," doParallel", "iterators","parallel","foreach"),repos="http://cran.ms.unimelb.edu.au/")
## On Mac OS
install.packages(c('sp','rgdal','spatstat','RColorBrewer','googleVis','rgeos'," doMC", "iterators","multicore","foreach"),repos="http://cran.ms.unimelb.edu.au/")